Objective To analyze the clinical value of computerized tomography (CT) and magnetic resonance imaging (MRI) in the diagnosis of rectal gastrointestinal stromal tumors. Methods The findings of CT and MRI of 24 patients with rectal gastrointestinal stromal tumors which was confirmed by pathology in our hospital during September 2011 to September 2014 were retrospectively analyzed. With the results of pathological examination as the standard, the accuracy, sensitivity and specificity of the two modes in the diagnosis of rectal gastrointestinal stromal tumors were compared. Results The probabilities of CT in the diagnosis of irregular tumors, tumor necrosis or cystic change, blurring tumor boundaries and metastasis to distant organs respectively were 58.33%, 37.5%, 62.5% and 25% while the probabilities of MRI diagnosis were 66.67%, 54.17%, 50% and 29.17% respectively. The accuracy of MRI was significantly higher than CT (91.67% vs 66.67%) (P<0.05). Conclusion The imaging findings of CT and MRI in the diagnosis of rectal gastrointestinal stromal tumors are different to certain degree. The detection rates of MRI to the compositions of lesions and the range of infiltration are higher than CT. CT and MRI examination can help to choose appropriate regimen.